Calculates false discovery rate estimates on crosslink identifications.

This tool calculates and FDR estimate for crosslink identifications, which are produced by OpenPepXL. The method employed currently is identical to the target-decoy approach used by xProphet (Walzthoeni et al., 2012). Consequently, this tool can also consume xquest.xml files (produced either by OpenPepXL or xQuest). The tool supports output in the idXML and mzIdentML formats.

Experimental classes:: This tool is work in progress and usage and input requirements might change.

pot. predecessor tools	$\longrightarrow$ XFDR $\longrightarrow$	pot. successor tools
OpenPepXL		OpenPepXLLF	-

The command line parameters of this tool are:

XFDR -- Calculates false discovery rate estimates on crosslink identifications
Version: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06
To cite OpenMS:
  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

Usage:
  XFDR <options>

Options (mandatory options marked with '*'):
  -in <file>                        Crosslink Identifications in either xquest.xml, idXML, or mzIdentML forma
                                    t (as produced by OpenPepXL) (valid formats: 'xml', 'idXML', 'mzid', 'xqu
                                    est.xml')
  -in_type <in_type>                Type of input file provided with -in (valid: 'xml', 'idXML', 'mzid', 'xqu
                                    est.xml')
  -out_idXML <idXML_file>           Output as idXML file (valid formats: 'idXML')
  -out_mzIdentML <mzIdentML_file>   Output as mzIdentML file (valid formats: 'mzid')
  -out_xquest <xQuestXML_file>      Output as xquest.xml file (valid formats: 'xquest.xml')
  -decoy_string <string>            Prefix of decoy protein ids. The correspondig target protein id should 
                                    be retrievable by deleting this prefix. (default: 'DECOY_')
  -minborder <minborder>            Filter for minimum precursor mass error (ppm). (default: '-1')
  -maxborder <maxborder>            Filter for maximum precursor mass error (ppm). (default: '-1')
  -mindeltas <mindeltas>            Filter for delta score, 0 is no filter. Minimum delta score required, 
                                    hits are rejected if larger or equal. (default: '0' min: '0' max: '1')
  -minionsmatched <minionsmatched>  Filter for minimum matched ions per peptide. (default: '0' min: '0')
  -uniquexl                         Calculate statistics based only on unique IDs.
  -no_qvalues                       Do not transform simple FDR to q-values
  -minscore <minscore>              Minimum score to be considered for FDR calculation (default: '0')
                                    
Common UTIL options:
  -ini <file>                       Use the given TOPP INI file
  -threads <n>                      Sets the number of threads allowed to be used by the TOPP tool (default: 
                                    '1')
  -write_ini <file>                 Writes the default configuration file
  --help                            Shows options
  --helphelp                        Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+XFDRCalculates false discovery rate estimates on crosslink identifications

version2.4.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'XFDR'

in Crosslink Identifications in either xquest.xml, idXML, or mzIdentML format (as produced by OpenPepXL)input file*.xml,*.idXML,*.mzid,*.xquest.xml

in_type Type of input file provided with -inxml,idXML,mzid,xquest.xml

out_idXML Output as idXML fileoutput file*.idXML

out_mzIdentML Output as mzIdentML fileoutput file*.mzid

out_xquest Output as xquest.xml fileoutput file*.xquest.xml

decoy_stringDECOY_ Prefix of decoy protein ids. The correspondig target protein id should be retrievable by deleting this prefix.

minborder-1 Filter for minimum precursor mass error (ppm).

maxborder-1 Filter for maximum precursor mass error (ppm).

mindeltas0 Filter for delta score, 0 is no filter. Minimum delta score required, hits are rejected if larger or equal.0:1

minionsmatched0 Filter for minimum matched ions per peptide.0:∞

uniquexlfalse Calculate statistics based only on unique IDs.true,false

no_qvaluesfalse Do not transform simple FDR to q-valuestrue,false

minscore0 Minimum score to be considered for FDR calculation

binsize0.0001 Bin size for the cumulative histograms for score distributions. Should be about the same size as the smallest expected difference between scores. Smaller numbers will make XFDR more robust, but much slower. Negative numbers are not allowed.1e-15:∞

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

forcefalse Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false